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- PDB-3abr: Crystal structure of ethanolamine ammonia-lyase from Escherichia ... -

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Basic information

Entry
Database: PDB / ID: 3abr
TitleCrystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl (substrate-free form)
Components(Ethanolamine ammonia-lyase ...) x 2
KeywordsLYASE / (beta/alpha)8 fold / Cobalt / Cobalamin
Function / homology
Function and homology information


ethanolamine ammonia-lyase / ethanolamine ammonia-lyase activity / ethanolamine ammonia-lyase complex / ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / cobalamin binding / amino acid metabolic process / cytosol
Similarity search - Function
Ethanolamine ammonia-lyase light chain (EutC), N-terminal domain / Ethanolamine ammonia-lyase light chain (EutC) / lyase / ethanolamine ammonia-lyase heavy chain domain like / Ethanolamine ammonia-lyase small subunit / Ethanolamine ammonia-lyase heavy chain / Ethanolamine ammonia-lyase light chain, C-terminal / Ethanolamine ammonia-lyase heavy chain, domain 2 / Ethanolamine ammonia-lyase heavy chain, N-terminal domain / Ethanolamine ammonia-lyase light chain (EutC) ...Ethanolamine ammonia-lyase light chain (EutC), N-terminal domain / Ethanolamine ammonia-lyase light chain (EutC) / lyase / ethanolamine ammonia-lyase heavy chain domain like / Ethanolamine ammonia-lyase small subunit / Ethanolamine ammonia-lyase heavy chain / Ethanolamine ammonia-lyase light chain, C-terminal / Ethanolamine ammonia-lyase heavy chain, domain 2 / Ethanolamine ammonia-lyase heavy chain, N-terminal domain / Ethanolamine ammonia-lyase light chain (EutC) / Ethanolamine ammonia lyase large subunit (EutB) / DNA Binding (I), subunit A / Ribosomal Protein L24e; Chain: T; / Annexin V; domain 1 / Aldolase class I / Aldolase-type TIM barrel / Roll / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COBALAMIN / Ethanolamine ammonia-lyase large subunit / Ethanolamine ammonia-lyase small subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShibata, N.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates.
Authors: Shibata, N. / Tamagaki, H. / Hieda, N. / Akita, K. / Komori, H. / Shomura, Y. / Terawaki, S. / Mori, K. / Yasuoka, N. / Higuchi, Y. / Toraya, T.
History
DepositionDec 21, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2012Group: Non-polymer description
Revision 1.3Feb 19, 2014Group: Database references / Derived calculations
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ethanolamine ammonia-lyase heavy chain
B: Ethanolamine ammonia-lyase light chain
C: Ethanolamine ammonia-lyase heavy chain
D: Ethanolamine ammonia-lyase light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,66419
Polymers165,2904
Non-polymers3,37415
Water18,0151000
1
A: Ethanolamine ammonia-lyase heavy chain
B: Ethanolamine ammonia-lyase light chain
C: Ethanolamine ammonia-lyase heavy chain
D: Ethanolamine ammonia-lyase light chain
hetero molecules

A: Ethanolamine ammonia-lyase heavy chain
B: Ethanolamine ammonia-lyase light chain
C: Ethanolamine ammonia-lyase heavy chain
D: Ethanolamine ammonia-lyase light chain
hetero molecules

A: Ethanolamine ammonia-lyase heavy chain
B: Ethanolamine ammonia-lyase light chain
C: Ethanolamine ammonia-lyase heavy chain
D: Ethanolamine ammonia-lyase light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)505,99257
Polymers495,86912
Non-polymers10,12345
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14500 Å2
ΔGint-48 kcal/mol
Surface area44720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)244.120, 244.120, 77.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
/ NCS ensembles :
ID
1
2

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Components

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Ethanolamine ammonia-lyase ... , 2 types, 4 molecules ACBD

#1: Protein Ethanolamine ammonia-lyase heavy chain / Ethanolamine ammonia-lyase large subunit


Mass: 49447.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2441, eutB, JW2434 / Plasmid: pUSI2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0AEJ6, ethanolamine ammonia-lyase
#2: Protein Ethanolamine ammonia-lyase light chain / Ethanolamine ammonia-lyase small subunit


Mass: 33197.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2440, eutC, JW2433 / Plasmid: pUSI2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P19636, ethanolamine ammonia-lyase

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Non-polymers , 4 types, 1015 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1000 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 6.0-7.0% (w/v) PEG 4000, 24-26 % (v/v) glycerol, 1.0 % (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1 M imidazole-HCl, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 3, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 144730 / Num. obs: 144730 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.5 / Num. unique all: 9260 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0087refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3ABO

3abo


Resolution: 2.1→42.29 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.841 / SU B: 12.464 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28519 7300 5 %RANDOM
Rwork0.24773 ---
obs0.24962 137417 94.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.382 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20.4 Å20 Å2
2--0.81 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10760 0 225 1000 11985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211154
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.99315160
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09451406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66824.362486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.687151880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5131584
X-RAY DIFFRACTIONr_chiral_restr0.2260.21748
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218380
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.11126986
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.191311230
X-RAY DIFFRACTIONr_scbond_it0.12624168
X-RAY DIFFRACTIONr_scangle_it0.19533930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1776tight positional0.080.05
22B944tight positional0.10.05
11C1610medium positional0.230.5
22D859medium positional0.350.5
11A1776tight thermal0.270.5
22B944tight thermal0.20.5
11C1610medium thermal0.282
22D859medium thermal0.242
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 494 -
Rwork0.285 9683 -
obs--89.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6225-0.2719-0.27482.00450.08071.00490.04220.0223-0.164-0.2601-0.010.490.08110.0544-0.03220.0652-0.0172-0.10190.04180.00740.208594.424-95.291-8.509
20.99950.4541-0.14282.5838-0.16530.2430.07610.2147-0.2375-0.7927-0.0470.95630.0519-0.1038-0.02910.4156-0.0146-0.49040.1744-0.10320.678374.3681-100.8788-27.1734
30.5076-0.33240.11422.0638-0.0431.05970.02190.0214-0.0541-0.00840.02220.5773-0.1222-0.0498-0.04420.0333-0.01030.00190.02880.0310.235586.288-60.189-2.715
41.4853-0.5457-0.10142.4822-0.38941.295-0.1255-0.1263-0.1220.77160.3531.5383-0.2896-0.4309-0.22750.30270.11020.48140.23610.20561.040765.454-64.00715.408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 453
2X-RAY DIFFRACTION2B44 - 295
3X-RAY DIFFRACTION3C1 - 453
4X-RAY DIFFRACTION4D44 - 295

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